The 1st thing that comes to mind on this is.......
if this occurred while the car was/is (still) in their care why is it that they can't solve the issue on their own?
If the car is equipped with light sentry then they should have applied the park brake to keep the lights off while it was/is in their shop, that way the battery wouldn't have been drained.
It's not necessary to remove the battery from the car to recharge it, if one wants to protect the PCM one just pulls the PCM fuse, it should be a 15a fuse, like most 1st gen W's it's in the glove box.
What you should have is Passkey II, there is a relearn cycle that has to be performed on the Vats module to let you restart the engine.